ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.1667T>G (p.Leu556Trp)

gnomAD frequency: 0.00003  dbSNP: rs200449833
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187780 SCV000241377 likely benign not specified 2016-07-07 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001852463 SCV002314128 uncertain significance Koolen-de Vries syndrome 2021-10-03 criteria provided, single submitter clinical testing This sequence change replaces leucine with tryptophan at codon 556 of the KANSL1 protein (p.Leu556Trp). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and tryptophan. This variant is present in population databases (rs200449833, ExAC 0.03%). This variant has not been reported in the literature in individuals affected with KANSL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 205792). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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